/*****************************************************************************/
/*                                                                           */
/* UNIT: NTL3_Abs_To_Human  (Level 3 library routine)                        */
/*                                                                           */
/* Author: Nikola Stojanovic                                                 */
/*                                                                           */
/* Revision:    07 SEP 94   Version 1.0                                      */
/*                                                                           */
/* Function:                                                                 */
/*                                                                           */
/*   Procedure determines the corresponding positions in the human sequence  */
/* for the given list of "absolute" intervals, with respect to the received  */
/* alignment file (name provided as an input parameter); returns the         */
/* "standard" error structure, NULL if there were no errors                  */
/*                                                                           */
/*****************************************************************************/


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "ntl3.h"




/*****************************************************************************/
/*                                                                           */
/* Definitions section                                                       */
/*                                                                           */
/*****************************************************************************/


/*****************************************************************************/
/* Definitions of global (static) variables of the unit                      */
/*****************************************************************************/


static int alignment_loaded = 0;            /* No alignment initially loaded */

static header_ptr file_data = NULL;        /* Contents of the alignment file */
static align_ptr alignment = NULL;           /* Partially unpacked alignment */

/*****************************************************************************/
/*                                                                           */
/* Code section                                                              */
/*                                                                           */
/*****************************************************************************/

/*****************************************************************************/
/*                                                                           */
/* PROCEDURE: NTL3_Abs_To_Human                                              */
/*                                                                           */
/* Central procedure for the unit; returns NULL if the alternative offset    */
/*   has been found and returned, diagnostic string otherwise                */
/*                                                                           */
/* Procedure abs_to_human determines offsets of pairs of positions specified */
/*   as absolute within the alignment, with respect to "humhbb_orig";        */
/*   positions are calculated as close as possible, and error made (if any)  */
/*   is returned together with offsets                                       */
/*                                                                           */
/* ASSUMPTION: Only one sequence in the alignment is "human"                 */

errind NTL3_Abs_To_Human (char *alignment_file, twoint_ptr absolutes,
                          fourint_ptr *offsets)
{
 errind load_status;

 /* Check whether this is the first invocation of this routine:              */
 /* Check whether the current alignment has already been loaded internally   */

 if (alignment_loaded == 0) {                     /* No alignment loaded yet */

  /* Load the contents of the specified alignment file in appropriate format */
  /*   into internal structure first                                         */

  if ((load_status = NTL2_Load_AlignFile (alignment_file, &file_data)) != NULL)
   return load_status;
  else {      /* Data from the file loaded, now partially expand alignment 1 */
   if ((load_status = NTL1_Load_Alignment (1, file_data, &alignment)) != NULL)
    return load_status;
   else alignment_loaded = 1;    /* Record that alignment data is now loaded */
  }
 }
 /* Now when it is guaranteed that both origins and alignments are loaded,   */
 /*   proceed to determine the desired corresponding positions in "human"    */

 return NTL1_Abs_To_Human (absolutes, file_data, alignment, offsets);
}